System for conducting the identification of bacteria in biological samples

ABSTRACT

The present invention relates to a system for conducting the identification and quantification of micro-organisms, e.g., bacteria in biological samples. More particularly, the invention relates to a system comprising a cooling, heating and fan arrangement for maintaining a predetermined optimum temperature of the samples during testing; a visual, circumferential and axial alignment system for aligning the samples within the carousel; a transfer system for transferring the samples from the carousel to the centrifuge; a balancing system of minimizing the rotational vibrations of the centrifuge; a safety system and anti-tipping design for the sample containing system; liquid dispensing arms for dispensing the buffered saline solution; and discharge ports for discharging and disposing of the liquid removed from the samples to a location external of the system.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.12/885,993, filed Sep. 20, 2010, now U.S. Pat. No. 10,288,632, whichclaims priority from U.S. Provisional Patent Application No. 61/244,118,filed Sep. 21, 2009, which is incorporated herein by reference.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates to a system for conducting theidentification and quantification of micro-organisms, e.g., bacteria inbiological samples such as urine. More particularly, the inventionrelates to a system comprising a cooling, heating and fan arrangementfor maintaining a predetermined optimum temperature of the samples priorto and during testing; a visual, circumferential and axial alignmentsystem for aligning the samples within a carousel; a transfer system fortransferring the samples from a carousel to a centrifuge; a balancingsystem of minimizing the rotational vibrations of a centrifuge; a safetysystem and anti-tipping design for the sample containing system; liquiddispensing arms for dispensing a buffered saline solution; and dischargeports for discharging and disposing of liquid removed from the samplesexternal of the system.

Description of Related Art

In general, current-day practice for identifying micro-organisms, e.g.,bacteria in urine samples, involves a complex, lengthy, and expensiveprocess for identifying and specifying micro-organisms in microbiologylabs. In the current process, the samples are accepted into the lab.These specimens are then sorted, labeled, and then are inoculated ontoblood agar medium using a sterilized loop. The specimens are theninserted into a dedicated incubator for a 24-hour period. A day later,the lab technicians screen the specimens for positive and negativecultures. In general, most of the cultures are negative and they aremanually reported. The organisms for the positive cultures are isolatedand suspended in a biochemical fluid. This involves suspension,dilution, vortexing, and turbidity measurements resulting in biochemicalwaste products. The cultures are then subjected to a speciesidentification and antibiotics susceptibility testing exposing thesuspensions to multiple reagents. After another 6 to 24-hour incubationperiod, the findings are interpreted and reported by lab technicians.This entire process generally takes 11 steps and 50 hours to obtainspecimen results and the process is labor intensive.

Commonly owned U.S. Patent Application Publication No. US/2007/0037135A1, the contents of which are herein incorporated by reference,discloses a system for identification and quantification of a biologicalsample suspended in a liquid. As disclosed in the reference sample,cuvettes are used for holding the biological sample. The referencestates that these cuvettes are said to be well-known in the art, aretypically square or rectangular in shape (having a well area to containthe sample), and are made of a transparent material such as glass or apolymeric material. However, the reference fails to disclose anyspecific description/design of the cuvettes.

There is a need, therefore, particularly for species identification ofthe above lab procedure to provide a more efficient and less timeconsuming process which requires less labor.

SUMMARY OF THE INVENTION

The system of the invention streamlines the current system for obtainingspecimen results. The system is environmentally friendly, enables arapid diagnosis, results are consistent, do not require reagents, andprovides for a multifunctional diagnosis. According to one embodimentdisclosed in commonly owned PCT Patent Application No. US/2008/079533,biological samples are contained within disposable cartridges. Thecartridges are bar coded and tied in with the patient's ID. Thecartridges are inserted in a magazine which is then inserted into asample processor which processes the specimens. The prepared specimensare transferred into the optical cuvettes and then the magazine isinserted into an optical analyzer which analyses the specimens. Theoptical analyzer analyses and generates the complete results enablingultimate treatment of the bacteria. The system does not require asophisticated operator and gives rapid results.

According to a first aspect, the invention is directed to a system forcooling and controlling the temperature of samples in a plurality ofoptics cups in an optical analysis. The system includes a carousel forsupporting a plurality of disposable cartridges, each cartridgesupporting a disposable optics cup containing a sample to be opticallyanalyzed by an optical analyzer. The carousel has a plurality of inletopenings and outlet openings, each associated with one of the disposablecartridges. The system further includes a turntable having a pluralityof inlet openings and outlet openings, each associated with one of theinlet openings and outlet openings in the carousel. An insulation plateis located below the turntable and includes at least one thermalelectrical cooler for cooling the air circulated through the inletopenings and outlet openings from the carousel through the turntable forcontrolling the temperature of the samples. The turntable includes a topplate and a bottom plate separated by a spacer and the optics cups andthe disposable cartridges are plastic such that convective coolingthrough the turntable and the plastic of the disposable cartridges andthe optics cups occurs for the rapid cooling of the specimens in theoptics cups. According to one design, the system for cooling andcontrolling the temperature of samples is located in an optical analyzerand is adapted to cool the samples to a desired temperature and tosubstantially maintain the temperature of the samples at the desiredtemperature until the processing of the samples in the optical analyzeris completed.

According to another aspect, the invention is directed to a system forpreventing contamination of samples held within a magazine. The systemcomprises a magazine for supporting a plurality of disposablecartridges, each cartridge being configured for supporting a containerincluding a sample to be analyzed, a cover configured for cooperatingwith the magazine for sealing a top portion of the magazine, and atleast one locking member for holding the cover in place. The system alsoincludes a handle removably attached to the cover.

According to another aspect, the invention is directed to an alignmentsystem for aligning samples within a magazine. The alignment systemcomprises at least one notch extending inwardly with respect to an outeredge surface of the magazine, a quality control cartridge locatedadjacent the at least one notch and a sensor for detecting the locationof the notch and the quality control cartridge. The notch and qualitycontrol cartridge provide a fixed location at which to initializetesting and functions as an initialization point for the cartridgescontained within the magazine. The alignment system can also include aquality control opening within the magazine. This quality controlopening is configured for receiving the quality control cartridge.Radial alignment indicia can be located on a top surface of a base plateof the magazine to provide a visual reference with respect to cartridgeplacement within magazine openings. The quality control cartridge canalso provide a testing reference to ensure properly functioning testingequipment.

According to another aspect, the invention is directed to a method forcircumferentially aligning samples within a magazine to optimize areflected signal of the samples. The magazine includes a carousel baseassembly and the method comprises applying light to a sample, providinga member to measure the light reflectance from the sample, and rotatingthe carousel base assembly back and forth along an approximate 9° arcuntil the light reflectance signal is maximized.

According to still another aspect, the invention is directed to ananti-tipping system for a rack assembly holding a plurality of storagedrawers for use within a sample processor. The rack assembly comprises aplurality of vertical and horizontal rails configured for holding thestorage drawers and a base rail. The anti-tipping system comprises atleast one extendable/retractable leg configured for extending from thebase rail. The anti-tipping system can include a locking mechanism forpreventing more than one storage drawer from being pulled out at onetime.

According to another aspect, the invention is directed to a method forpreventing crystallization of samples within a sample processorcomprising providing a heating device for heating the samples containedwithin the magazine and maintaining the samples at a desiredtemperature. Preferably the samples are maintained at approximately 37°C., or body temperature.

According to still another aspect, the invention is directed to afan/filter arrangement for use in a processor unit for conductingtesting of biological samples. The arrangement comprises a fan forpassing air into and through the processor unit wherein the air has apredetermined temperature for maintaining the predetermined temperaturewithin the unit. The arrangement further comprises a filter forfiltering the air as it passes therethrough and out of the processorunit and a feedback control loop for adjusting a speed of the fan tomaintain the air at the predetermined temperature within the processorunit. Preferably the fan is a HEPA fan. The arrangement can include apressure sensor located adjacent to the filter to measure a pressuredrop exiting through the filter to indicate a need for filterreplacement.

According to another aspect, the invention is directed to a processorunit for use with a biological testing system. The processor unitcomprises a heating system for heating the samples to a predeterminedtemperature; a fan/filter arrangement for maintaining the samples at thepredetermined temperatures; and a transfer arm arrangement fortransferring a tube from a magazine to a centrifuge. The transfer armarrangement can comprise a 6-bar linkage wherein the 6-bar linkagecomprises a pair of arms adapted for being positioned at opposite sidesof the magazine and wherein each arm includes a pair of grippersconfigured for moving two tubes at one time, allowing for the totalmovement of four tubes from the magazine to the centrifuge at one time.Each arm can include an optical sensor to locate the position of thetubes. The grippers can be configured for axial adjustment according tospacing differences of the tube locations as held within the magazineand the positioning openings in the centrifuge.

According to another aspect, the invention is directed to a method forreducing vibration of a partially filled centrifuge comprising providingat least one balance tube and strategically positioning the at least onebalance tube within the centrifuge to balance and distribute the weightof the centrifuge to reduce vibration thereof during rotation. The atleast one balance tube has a weighted bottom portion such that theoverall weight of the tube is substantially equal to the weight of atube containing a sample. A computer controlled system can be providedto determine the optimum placement locations for the sample containingtubes and the at least one balance tube.

According to another aspect, the invention is directed to a liquiddispensing arm for use with a processor unit in a biological testingsystem. The liquid dispensing arm includes a first end associated with aprocessing fluid, a second end associated with a tube, and a pump forpumping said processing fluid into said tube. The pump is adapted forapplying a suctioning force to remove the processing fluid from thetube. At least one discharge port is provided for discharging thewithdrawn processing fluid and disposing the fluid at a locationexternal to the processor unit. The arm and discharge port can pivotwith respect to the tube to allow for removal of the tube. A heater canbe provided for heating the processing fluid to a predeterminedtemperature prior to dispensing the fluid into the tube.

In one embodiment, the present invention relates to a system including aplurality of disposable cartridges wherein each of the cartridgesincludes four disposable components including a centrifuge tube, a firstpipette tip having a 1 ml volume, an optical cup or cuvette, and asecond pipette tip having a 0.5 ml volume. According to another design,the optics cup or cuvette may be a rectangular-shaped container, andpreferably an injection molded plastic having an upper rectangularopening and a tapered area extending inwardly and downwardly relative tothe rectangular opening. The optics cup or cuvette holds a sample, e.g.,biological sample, chemical sample, or toxicant sample, e.g., urine foroptical analysis. If the sample is a urine sample, then the opticalanalysis would be for micro-organism or organisms, e.g., bacteria in theurine.

In one embodiment, the system includes a plurality of disposablecartridges for holding a plurality of disposable components including: acentrifuge tube; a pipette tip; and an optical urine sample cuvette; asample processor for receiving the plurality of disposable cartridgesand configured to process and prepare the urine sample of eachdisposable cartridge and to transfer the urine samples into therespective optical cuvette of each of the disposable cartridges; and anoptical analyzer for receiving the cartridge with the optical cuvettescontaining the processed urine samples and analyzing and generating thespecimen results. The entire process of processing the urine specimensin the sample processor and analyzing them in the optical analyzer takesabout 30 minutes for a single specimen and up to 2 hours for 42specimens.

The disposable cartridge and the disposable components of the presentinvention provide advantages over the currently used cartridges andcomponents as they increase efficiency, improve workload and save timeand money since the components necessary for the preparation orprocessing of the urine samples are conveniently located in one place,i.e., in a cartridge. Additionally, less manpower or manual handling ofthe components is required for the processing/analyzing of the urinesamples. There is also the added convenience in that the cartridge andits components are disposable. That is, these items do not need to besterilized for the next urine specimen identification process andcontamination of the work area and/or surrounding environment isminimized.

According to another aspect of the invention, there is provided a systemfor cooling and controlling the temperature of a sample, e.g., urinesample in an optics cup or cuvette for optical analysis, and the systemmay be located in an optical analyzer which performs analysis of one ormore samples.

The turntable, preferably, is made of aluminum, and the optics cups orcuvettes and disposable cartridges are preferably made of plastic,thereby enabling convective cooling to occur through the aluminummaterial and the plastic material for rapidly cooling the specimens andthen maintaining the specimens at a desired temperature during theoptical analysis of the specimens or samples.

In one embodiment, the present invention provides a system for coolingand controlling the temperature of the samples being subjected to anoptical analysis so that the signal of the specimens may be maintainedfor an adequate analysis of the organisms in the specimens.

In an additional embodiment, the fluid sample may be, for example, abiological, chemical or toxicant sample, e.g., urine sample which isoptically analyzed, for example, for the type and amount of organism ormicro-organism, e.g., bacteria in the sample.

These and other objects and advantages of the invention will be madeapparent from the following description taken together with thedrawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a top perspective view of a magazine having a plurality ofdisposable cartridges.

FIG. 1B is a top perspective view of a disposable cartridge used in themagazine shown in FIG. 1A.

FIG. 2 is a front sectional view illustrating the components of thedisposable cartridge of FIG. 1B in phantom.

FIG. 3A is a perspective view of a sample processor illustrating inphantom the several components of the sample processor of the system ofthe invention.

FIG. 3B is an additional perspective view of a sample processorillustrating in phantom the several components of the sample processorof the system of the invention.

FIG. 4A is a perspective view of an optical analyzer illustrating inphantom the several components of the optical analyzer of the system ofthe invention.

FIG. 4B is a perspective view of an optics system illustrating inphantom the several components of the optics of the system of theinvention.

FIG. 4C is an additional perspective view of an optical analyzerillustrating in phantom the several components of the optical analyzerof the system of the invention.

FIG. 5 is a schematic illustrating mirrored convex “horn” that may beprovided at the entrance of a slit of a spectrometer.

FIG. 6 is a perspective view of a centrifuge illustrating in phantom theseveral components of the centrifuge of the system of the invention.

FIG. 7 is an additional perspective view of a sample processorillustrating in phantom the several components of the sample processorof the system of the invention.

FIG. 8A is a perspective view of a disposable cartridge according to analternative embodiment of the invention for supporting the disposablecomponents including an optics cup.

FIG. 8B is a cross sectional view taken along line IX A-IX A,illustrating the disposable cartridge of FIG. 8A and the disposablecomponents, including an optics cup which is shown in phantom.

FIG. 8C is a top perspective view of a magazine having a plurality ofthe disposable cartridges of FIGS. 8A and 8B.

FIG. 8D is a perspective view of the disposable cartridge withoutdisposable components of FIG. 8A showing attachment clips for securingthe cartridge within the magazine.

FIG. 8E is a side elevation view of the cartridge of FIG. 8D.

FIG. 8F is an opposite side elevation view of the cartridge of FIG. 8D.

FIG. 9A is a perspective view illustrating an optics cup of the presentinvention with an aluminum ribbon liner partially covering the innersurface of the container of the optics cup.

FIG. 9B is a perspective view illustrating an optics cup of the presentinvention with an aluminum liner totally covering the inner surface ofthe container.

FIG. 9C is a partially enlarged perspective view illustrating a portionof the ribbon liner of FIG. 9A attached via a crimping process to aflange of the optics cup of the present invention.

FIG. 10 is a top plan view illustrating the inner surface of thecontainer of FIGS. 9A and 9B as being coated with an aluminum coating.

FIG. 11A is a partially enlarged perspective view illustrating theribbon liner of FIG. 9A being attached to the container via a one-wayretention tab.

FIG. 11B is a perspective view illustrating the ribbon liner of FIG. 9Abeing attached to the container via heat staked pins.

FIG. 11C is an enlarged partial perspective view illustrating the ribbonliner of FIG. 9A being attached to the container via a snap mechanism.

FIG. 12 is a perspective view illustrating a further embodiment for arectangular-shaped container of the present invention.

FIG. 13A is a schematic view according to one design of the inventionillustrating the pathways for air jets provided in a cooling system ofthe invention and involves liquid cooling that is converted into airflow cooling.

FIG. 13B is a schematic view according to another design of theinvention illustrating the pathways for air jets for cooling thesamples.

FIG. 14A is a top perspective view, utilizing the cooling system of FIG.13A, showing a carousel supporting a disposable cartridge, which inturn, is carrying a disposable optics cup and a plurality of airpassageways in the carousel.

FIG. 14B is a bottom perspective view of the carousel of FIG. 14A.

FIG. 15A is an expanded perspective view of a cold chamber assemblyutilizing the cooling system of FIG. 13B.

FIG. 15B is a top perspective view of the cold chamber assembly of FIG.15A.

FIG. 15C is a bottom perspective view of the cold chamber assembly ofFIG. 15A.

FIG. 15D is a perspective view of the bottom plate of the cold chamberassembly of FIG. 15A.

FIG. 15E is a top perspective view of the top plate of the cold chamberassembly of FIG. 15A.

FIG. 15F is a top view, utilizing the cooling system of FIG. 13B,showing a carousel supporting a disposable cartridge, which in turn, iscarrying a disposable optic cup and a plurality of air passageways inthe carousel.

FIG. 16 is a schematic illustration of an arrangement of components fora spectrometer.

FIG. 17 is a graph illustration of the response of a grating used in thearrangement of FIG. 16 plotting the absorbance efficiency versus thewavelength of the illumination beam.

FIG. 18 is a perspective view illustrating an illumination arrangementof the optical reader of the invention.

FIG. 19 is an illustration showing the path of travel of the light beamfrom the light source to the specimen produced by the illuminationarrangement of FIG. 18.

FIG. 20 is a graph illustrating reflectance versus wavelength of theturning mirror within the illumination arrangement of FIG. 18.

FIG. 21 is a schematic illustrating an optics cup positioned in theillumination arrangement of FIG. 18.

FIG. 22A shows a top view of a cover assembly for use with the magazineof FIG. 1A.

FIG. 22B shows a cross-sectional view taken along line B-B of the coverassembly of FIG. 22A.

FIG. 23A shows an expanded perspective view of the carousel baseassembly including an alignment notch according to the presentinvention.

FIG. 23B is a top view of the carousel base assembly of FIG. 23A.

FIG. 23C is a top view of the base plate of the carousel base assemblyof FIG. 23A.

FIG. 23D is an enlarged view of the alignment notch taken from sectionalportion “d” from FIG. 23C.

FIG. 24A is a perspective view of a rack assembly used in the sampleprocessor wherein the rack assembly includes an anti-tipping feature.

FIG. 24B is a schematic view of the rack assembly of the sampleprocessor of FIG. 24A.

FIGS. 25A-25C are perspective, side, and top views, respectively of theheater assembly for heating the samples in the processor unit.

FIG. 26A is a cross-section view of a balance tube for use within thecentrifuge.

FIG. 26B is an enlarged view encircled by “B” in FIG. 26A;

FIG. 27A is a back elevation view of the fan/filter arrangement for usewithin the processor unit;

FIG. 27B is a side elevation view of the fan/filter arrangement of FIG.27A.

FIG. 27C is a top view of the fan/filter arrangement of FIG. 27A.

FIG. 27D is a front perspective view of the fan/filter arrangement ofFIG. 27A including a back door.

FIG. 27E is a back elevation view of the fan/filter arrangement of FIG.27A with the back door removed.

FIG. 27F is a back expanded perspective view of the fan/filterarrangement of FIG. 27A.

FIG. 28A is a perspective view of the 6-bar linkage transfer system.

FIG. 28B is a side elevation view of a carousel including a pair oftransfer arms.

FIG. 28C shows a schematic view of the gripper mechanism for use withthe transfer system of FIG. 28A.

FIG. 28D shows the change in circumferential spacing from the carouselto the centrifuge.

FIG. 29A shows a side elevation view of a dispensing arm for dispensingbuffered saline solution and suctioning liquid.

FIG. 29B shows a schematic view of dispensing arms/discharging portslocated with respect to the carousel for discharging liquid externalfrom the system.

FIG. 29C shows the discharge ports of FIG. 29B including a pump fordischarging the liquid.

DETAILED DESCRIPTION OF THE INVENTION

The present invention will be described with reference to theaccompanying drawings where like reference numbers correspond to likeelements.

For purposes of the description hereinafter, spatial or directionalterms shall relate to the invention as it is oriented in the drawingfigures. However, it is to be understood that the invention may assumevarious alternative variations, except where expressly specified to thecontrary. It is also to be understood that the specific componentsillustrated in the attached drawings, and described in the followingspecification, are simply exemplary embodiments of the invention. Hence,specific dimensions and other physical characteristics related to theembodiments disclosed herein are not to be considered as limiting.

FIGS. 1A-7 disclose “A System for Conducting the Identification ofBacteria in Urine” set forth in PCT Patent Application No. US2008/079533, filed on Oct. 10, 2008, which is commonly owned and hereinincorporated by reference in its entirety. Referring to FIGS. 1A, 1B, 2,3A, 3B, 4A-4C, the system for conducting the identification of bacteriain urine samples includes a disposable cartridge 12 (FIGS. 1B and 2); asample processor 14 (FIGS. 3A, 3B, 6 and 7); and an optical analyzer 16(FIGS. 4A, 4B, and 4C). As shown in FIGS. 1A and 2, cartridge 12contains four disposable components, which are a centrifuge tube 18, afirst pipette tip 20 having a 1 ml volume, an optical cup or cuvette 22,and a second pipette tip 24 having a 0.5 ml volume. It is to beunderstood that the presently described inventive system is appropriatefor the identification of bacteria in any fluid and is not limited tobacteria samples contained in urine.

The centrifuge tube 18 is a container that has an elongated body 18 bwith a tapered end indicated at 18 a. In general, the centrifuge tube 18initially contains the urine sample and the first pipette tip 20 may beused to dilute the urine-dissolved constitutes, and the second pipettetip 24 may be used to transfer the diluted urine sample into the opticalcup or cuvette 22 for optical analysis. The disposable cartridge 12 andits disposable components 18, 20, 22, and 24 may be made of a plasticmaterial which is easily molded and inexpensive to manufacture.

Still referring to FIG. 2, the disposable components 18, 20, 22, and 24are each contained within separate locations 30, 32, 34, and 36,respectively, of the disposable cartridge 12. As is shown, the bottom ofcompartment 32 which receives and carries the first pipette tip 20 isclosed so that any drip from the first pipette tip 20 will notcontaminate the surface below the disposable cartridge 12. Eachcomponent 18, 20, 22, and 24 is suspended within its respective location30, 32, 34, and 36 via a lip 40, 42, 46, and 48, respectively, attachedto each component 18, 20, 22, and 24, which is supported by the topsurface 50 of disposable cartridge 12.

Referring to FIGS. 2 and 4A, an optical cup or cuvette 22 may be used inthe optical analyzer 16 of FIG. 4A. Preferably, the urine samples areprepared with a saline solution since saline solutions minimizebackground fluorescence, while maintaining the integrity of thebacteria, which is particularly important when using optics in the urineanalysis process. The optical cup or cuvette 22 will include areflective coating to assist in the optical analysis. The optical cup orcuvette 22 may be made of an ABS plastic material, glass or a metallicmaterial, e.g., aluminum, and then coated with or layered with thereflective material. Alternatively, in the manufacturing of the opticalcup or cuvette 22, the layer of reflective material may be incorporatedonto the plastic, glass or metallic material. As best shown in FIG. 2,the optical cup or cuvette 22 includes a tapered end indicated at 22 ain order to assist with the optical analysis. It is anticipated that theUV-light source in the optical analyzer 16 (FIGS. 4A, 4B and 4C) bedirected down the middle of the optical cup or cuvette 22 for theoptical analysis of the urine specimen in the optical cup or cuvette 22.

Several disposable cartridges 12, each containing the four disposablecomponents 18, 20, 22, and 24 are then inserted into a magazine 26 shownat the top of FIG. 1A, which is then loaded into the sample processor 14as shown in FIG. 3A. Magazine 26 contains several disposable cartridges12, some of which are numbered, each cartridge 12 having a unique barcode as indicated at 28 in FIG. 1A that is paired with the specimen of apatient. Alternatively, the magazine 26 can then be inserted into adevice for the optical analysis of the urine samples. Preferably, thesame magazine 26 used in obtaining processed urine samples in a sampleprocessor is used in the device for the optical analysis of theprocessed urine samples.

The sample processor 14 of FIGS. 3A and 3B contains a centrifuge 31, acarousel 15 containing several disposable cartridges 12; a rotatabletable 41 supporting the carousel 15; an optical cuvette 22; a rotatablegripper mechanism 33 which picks up the centrifuge tube 18 (FIGS. 1A and1B) of each disposable cartridge 12 and inserts the centrifuge tube 18into the centrifuge 31; two movable fluid transfer arms 35, 35 a, whichare used to dilute the dissolved material in the urine samples via thepipette tip 20 (FIGS. 1B and 2), and to transfer the diluted sample tothe optical cup or cuvette 22 (FIG. 2) via the pipette tip 24; and asyringe pump dispenser fluid system 37 for delivering water to thesamples for dilution purposes. The sample processor 14 also includes adrawer 38 which has a rotatable table 41 which receives, supports, androtates the magazine 26 when the drawer 38 is inserted into the sampleprocessor 14. The drawer 38 contains a magazine drive mechanism (notshown) which rotates the magazine 26. The sample processor additionallyincludes a centrifuge 31 for receiving centrifuge tubes 18 forcentrifuging the samples in the tubes 18; two movable fluid transferarms 35 and 35 a for diluting the dissolved material in the saline; anda syringe pump dispenser fluid system 37 for delivering clean fluid tothe samples for the dilution of the samples. Control unit 27 shown tothe right of FIG. 3A houses controls for ventilation, filtration andpower management for the sample processor 14.

The sample processor 14 also includes a drawer 38 for inserting carousel15 into the sample processor 14, a bar code reader 58 for identificationof cartridges 12, a pipetting system 43, and a metering system 45 formanaging the pipetting system 43 and dispenser fluid system 37.

In general, centrifuge tube 18 contains about a 2 ml sample of filteredurine which is placed into the centrifuge tube by the user. This samplemay then be sufficiently diluted with a saline solution or water bycentrifuging the sample, followed by using the first pipette tip 20 withthe 1.0 ml volume to decant the supernates in two decant cycles followedby refilling of the centrifuge tube 18 with saline or water. The secondpipette tip 24 having the 0.5 ml volume may then be used to draw outabout 500 μl of fluid from centrifuge tube 18 and then to dispense this500 μl of fluid into the respective optical cup or cuvette 22 of thedesignated patient. This second pipette tip 24 can then be inserted intothe first pipette tip 20 and both pipette tips 20, 24 can be disposed ofproperly. It is believed that one pipette tip may be used to dilute anddraw out instead of two pipette tips. This process may be done manuallyor may be done automatically.

The loading and unloading of the magazine 26 is accomplished with theseveral disposable cartridges 12 mounted on the rotatable table 41 (FIG.1A). The manual drawer contains a magazine drive mechanism (not shown).Once the magazine 26 is inserted into the sample processor 14, the drivemechanism (not shown) for rotatable table 41 rotates the magazine 26;the bar code reader (element 58 in FIG. 4A) inventories the samples, alevel sensor (not shown) verifies that samples were dosed properly; anda second sensor (not shown) verifies that all of the necessarydisposable components 18, 20, 22, and 24 (FIG. 2) are contained in eachdisposable cartridge 12.

The transfer of the centrifuge tube 18 (FIG. 2) into the centrifuge 31(FIGS. 3A and 3B) will now be described. A centrifuge lid 31 a of thecentrifuge 31 is oriented to allow the rotatable gripper mechanism unit33 to access and load the centrifuge 31. The drive mechanism of therotatable table 41 is configured to align the centrifuge tube 18 of eachdisposable cartridge 12 into position relative to the rotatable grippermechanism unit 33. The gripper 33 a of rotatable gripper mechanism 33selects the centrifuge tube 18 for transfer from the magazine 26 andinto the centrifuge 31. The centrifuge rotor (not shown) is configuredto align a vacant centrifuge holder of centrifuge 31 in the loadposition. The gripper 33 a referred to as a “Theta Z gripper” is aradial member that rotates and has a downward and upward movement forpicking up and setting a centrifuge tube 18 into a vacant centrifugeholder of centrifuge 31. The lid 31 a of centrifuge 31 is closed afterall of the centrifuge tubes 18 are placed into the centrifuge 31.

Centrifuge 31 (FIG. 6) is automatically operated to spin the centrifugetubes 18 at about a 12,000 g-force for about 2 minutes. The centrifuge31 includes tube holders that are configured to swing each of thecentrifuge tubes 18 about 90° upon rotation of the centrifuge 31. Thecentrifuge allows for precise positioning and position tracking so thatcorrect tubes are returned to cartridges in the magazine aftercentrifugation. This action results in the solid formation of thebacteria present in the urine sample at the bottom of the centrifugetube 18.

There are two fluid transfer arms 35, 35 a (FIGS. 3A and 3B) forremoving the supernates from two samples of two disposable cartridges 12at a time. After the two fluid transfer arms 35, 35 a (FIGS. 3A and 3B)obtain the pipette tip 20 (FIG. 2) with a 1 ml volume, each of the fluidtransfer arms 35 and 35 a (FIGS. 3A and 3B) makes two consecutive tripsto the centrifuge tube 18, each time drawing fluid from the tube 18 anddispensing this fluid into a waste port (not shown) of sample processor14 before returning the pipette tip 20 to its location on the disposablecartridge that is being sampled and before continuing with the nextsample in the disposable cartridge 12 that is rotated to be registeredin the sampling location of sample processor 14.

The syringe pump dispenser fluid system 37 is illustrated in FIG. 7, fordelivering water or saline to the samples for dilution purposes. Thewaste fluid which had been decanted from a centrifuge tube 18, asdescribed in the preceding paragraph, is replaced with clean processfluid via system 37. Two syringe pumps dispense this clean process fluidinto the centrifuge tube 18 from which the waste fluid had been removedin the previous step. During the final refill step, a smaller amount ofclean fluid is used in order to get the bacteria level in the centrifugetube 18 to the required concentration.

After the sample in centrifuge tube 18 has been sufficiently dilutedwith the clean fluid, one of the two fluid transfer arms 35, 35 a (FIGS.3A and 3B) transfers the processed sample in centrifuge tube 18 to theoptical cup or cuvette 22 of its respective disposable cartridge 12. Oneof the fluid transfer arms 35, 35 a grasps the pipette tip 24 having the0.5 ml volume, which until now has not been used in this process. Thispipette tip 24 with the smaller volume is used to draw out about 500 μlof fluid from centrifuge tube 18 and is used to dispense this fluid intothe respective optical cup or cuvette 22 of the designated patient. Thispipette tip 24 with the smaller volume is then inserted into the pipettetip 20 with the larger volume via the fluid transfer arm 35 or 35 a fordisposal of both pipette tips 20, 24.

The metering/decanting, metering/refilling, and metering/fluidtransferring process described herein is to obtain preferably,approximately a 1,000,000:1 dilution of the dissolved materialsretaining bacteria in the urine sample in centrifuge tube 18. This canbe achieved by 1) centrifuging through means known to those skilled inthe art, the urine sample at a 12,000 g-force; 2) decanting about 95% ofthe fluid by using the first pipette tip 20; 3) replacing the decantedsolution of 2) with a saline solution; and 4) repeating steps 1), 2) and3) at least five times by using the first pipette tip 20. The finalprocessed urine sample in centrifuge tube 18 can then be decanted viathe second pipette tip 24 into the optical cup or cuvette 22.

The final processed urine sample in optical cup or cuvette 22 can thenbe used in an optical analysis for determining the micro-organism'sidentity and/or quantity in the urine sample in optical cup or cuvette22. This information can be obtained by using the system as disclosed inthe aforesaid U.S. Patent Application Publication No. 2007/0037135 A1.

Each of the steps described above for one centrifuge tube 18 is done inthe sample processor 14 for each of the disposable cartridges 12 inmagazine 26. It is to be appreciated that the waste fluid of eachdisposable cartridge 12 is disposed into a receptacle (not shown) insample processor 14, or is plumbed directly into a drain. The wastedisposables, i.e., the disposable cartridge 12 and disposable components18, 20, 22, and 24 remain on the magazine 26 for manual removal when themagazine 26 is unloaded in preparation for the next operation of thesample processor 14 for processing the next batch of urine samples.

The following steps are involved in processing the urine samples inpreparation for analysis via the optical analyzer 16 of FIGS. 4A, 4B,and 4C. In general, a sample of urine is obtained in a test tube. Thissample is passed through a 10 micron filter from which a 2 ml sample isobtained and placed into the centrifuge tube 18. The desired dilutedsample, i.e., 1,000,000:1 dilution of dissolved materials whileretaining bacteria in the urine sample is obtained by centrifuging this2 ml sample at about a 12,000 g-force; and decanting 95% of the fluid.This latter step is repeated five times wherein the decanted solution isreplaced each time with a saline solution. A saline solution is selectedfor this process in that it minimizes background fluorescence whichcomes into play when the processed urine sample is inserted into theoptical analyzer 16 while maintaining the bacteria integrity.

Referring to FIGS. 8A, 8B, and 8C, there is shown an alternativeembodiment for a disposable cartridge generally indicated as 112, whichmay be used for conducting the identification and quantification ofcontaminants, e.g., micro-organisms, bacteria in samples, urine samples.Disposable cartridge 112 contains and carries several disposablecomponents which include a centrifuge tube 118, a pipette tip 120 and anoptics cup or cuvette 122. With particular reference to FIG. 8B, thepipette tip 120 has a predetermined volume, for example, ranging between0.1 ml to about 10 ml, preferably 1 ml to 2 ml. The centrifuge tube 118is a container that has an elongated body 118 b with a tapered endindicated at 118 a. In general, the centrifuge tube 118 initiallycontains the sample and the pipette tip 120 may be used to dilute thedissolved sample constituents and then transfer the diluted urine sampleinto the optics cup or cuvette 122 for optical analysis. The disposablecartridge 112 and its disposable components 118, 120, and 122 may bemade of an ABS plastic material which is easily injection molded andinexpensive to manufacture.

Still referring to FIGS. 8A and 8B, the disposable components 118, 120,and 122 are each contained within separate compartments 130, 132, and134, respectively, of the disposable cartridge 112. As is shown, thebottom of compartment 132, which receives and carries the pipette tip120, is closed so that any drip from the pipette tip 120 will notcontaminate the surface below the disposable cartridge 112. Components118 and 120 are suspended within their respective compartments 130, 132via lips 140, 142, respectively. Lips 140 and 142 are attached to theirrespective components 118 and 120, and are supported by a top surface150 of disposable cartridge 112. In a similar manner, optics cup orcuvette 122 is suspended within its respective compartment 134 via aflange 154 of optics cup or cuvette 122 also supported by the topsurface 150 of disposable cartridge 112. The compartments 130 and 132are generally cylindrically shaped and extend substantially the lengthof centrifuge tube 118 and pipette tip 120. Compartment 134, forpositioning supporting optics cup or cuvette 122, is substantiallyenclosed within the disposable cartridge 112 and has a configurationsimilar to that of optics cup or cuvette 122.

The optics cup or cuvette 122 is a container and preferably includes areflective coating or layer to assist in the optical analysis. Theoptics cup or cuvette 122 is shown in FIGS. 9A and 9B and is discussedin further detail below. In particular, an inner surface of optics cupor cuvette 122 is coated with a reflective material or contains a layerof reflective material. The optics cup or cuvette 122 may be made of anon-reflective material, for example, an ABS plastic material or glass,or it may be made of a metallic material, e.g., aluminum. In the latterinstance, that is, if the optics cup or cuvette 122 is made of anon-reflective material, it may be coated with or layered with thereflective material. Alternatively, in the manufacturing of the opticscup or cuvette 122, the layer of reflective material may be incorporatedonto the plastic or glass. As best shown in FIG. 9A, the optics cup orcuvette 122 includes the lower tapered area indicated at 124 in order toassist with the optical analysis of the specimen, and it is anticipatedthat the UV-light source provided in an optical analysis be directedinto the optics cup or cuvette 122 for the optical analysis of thespecimen, more about which is discussed hereinbelow.

The disposable cartridge 112 preferably is injection molded and made ofan ABS plastic, preferably a non-reflective black colored plastic. Thedisposable cartridge 112 contains compartments 130, 132, and 134 forpositioning and supporting the centrifuge tube 118, pipette tip 120, andoptics cup or cuvette 122 discussed hereinabove. The compartments 130and 132 generally are cylindrical in shape so as to receive thecylindrical shapes of the centrifuge tube 118 and pipette tip 120 foradequate support of centrifuge tube 118 and pipette tip 120 within thedisposable cartridge 112. However, the compartment 134 for positioningand supporting the optics cup or cuvette 122, particularly if the opticscup or cuvette 122 is rectangular-shaped, need not be molded in the sameconfiguration as the optics cup or cuvette 122. In this instance, thecompartment 134 for supporting the optics cup or cuvette 122 indisposable cartridge 112 may, in general, include a rectangular-shapedopening 158 (FIG. 8A) located in the top surface 150 of the disposablecartridge 112 wherein the top flange 154 of optics cup or cuvette 122engages and is supported by the top surface 150 of disposable cartridge112 and the optics cup or cuvette 122 is suspended in the disposablecartridge. Alternatively, compartment 134 for positioning and supportingoptics cup or cuvette 122 may be totally enclosed and may have a similarconfiguration to that of rectangular-shaped optics cup or cuvette 122.

As discussed above and shown in FIG. 8C, several disposable cartridges112, each containing disposable components 118, 120, and 122, may beinserted into a magazine 126, which may then be inserted into a sampleprocessor 14, such as the processor shown in FIG. 3A. Each disposablecartridge 112 can have a unique bar code 128 which is paired with theinitial specimen of a patient. Alternatively, the magazine 126 may thenbe inserted into a device, such as the optical analyzer 16 shown in FIG.4A, for the optical analysis of the samples. Preferably, the samecarousel used in obtaining processed urine samples in a sample processoris used in the device for the optical analysis of the processed samples.

FIGS. 8D, 8E, and 8F show the disposable cartridge 112 without thedisposable components 118, 120 and 122 according to an embodiment of theinvention wherein attachment clips 113, 115, and 117 are provided. Theseattachment clips 113, 115, 117 extend in a horizontal direction along abottom edge portion of a side body portion 114 of the cartridge 112. Asshown in FIGS. 8D and 8E, attachment clip 115 may include a verticallyextending alignment member 116. This vertically extending alignmentmember 116 can be used for aligning the cartridge 112 during insertioninto the magazine 126. The attachment clips 113, 115, 117 are configuredto cooperate with the cartridge openings within the magazine 126, asshown in FIG. 8C, to form a snap fit arrangement therein to attach thecartridge 112 within this opening. Accordingly, in this embodiment, thecartridge openings within the magazine 126 can include appropriate clipopenings (not shown) which are configured to cooperate with the clips113, 115, 117 and alignment member 116 of the cartridge 112.

In general, centrifuge tube 118 may first contain, for example, between1 ml to about 2 ml sample of a filtered specimen. This sample may thenbe sufficiently diluted with a saline solution or water by centrifugingthe sample followed by using the pipette tip 120 to decant thesupernates in two decant cycles followed by refilling of the centrifugetube 118 with a saline or water. The pipette tip 120 may then be used todraw out a predetermined amount of fluid, e.g., 100 to 500 μl of fluidfrom centrifuge tube 118 and then to dispense this amount of fluid intoits respective optics cup or cuvette 122 of the designated patient.

The metering/decanting, metering/refilling and metering/fluidtransferring process described herein in the preceding paragraph may beused to obtain preferably, approximately a 1,000,000:1 dilution of thedissolved material in the sample while retaining contaminants, e.g.,bacteria in the sample, e.g., biological sample in centrifuge tube 118.This can be achieved by: 1) centrifuging, through means known to thoseskilled in the art, the sample at 12,000 g-force; 2) decanting about 95%of the fluid by using the pipette tip 120; 3) replacing the decantedsolution of step 2) with a saline solution; and 4) repeating steps 1),2), and 3) at least five times by using the pipette tip 120. The finalprocessed urine sample in centrifuge tube 118 can then be decanted viathe pipette tip 120 into the optics cup or cuvette 122.

The final processed sample in optics cup or cuvette 122 can then be usedin an optical analysis for determining the micro-organism's identityand/or quantity in the sample. This information can be obtained by usingthe system as disclosed in the aforesaid U.S. Patent ApplicationPublication No. 2007/0037135 A1.

FIGS. 9A and 9B illustrate an optics cup or cuvette, generally indicatedas 122, including a rectangular-shaped container 123 having a well 156and a rectangular opening 158 contiguous to well 156 for receiving afluid sample which is then carried in well 156. As stated above, theoptics cup or cuvette 122 may be made of glass or plastic, preferably,an injection molded plastic. The fluid sample may be, for example, abiological, chemical or toxicant sample, e.g., urine sample which isoptically analyzed, for example, for the type and amount of organism ormicro-organism, e.g., bacteria in the sample. Well 156 of container 123is formed by spaced-apart sidewalls 160 and 162, spaced-apart end walls164 and 166 and a floor 168. Spaced-apart sidewalls 160 and 162 andspaced-apart end walls 164 and 166 form a flange 170 contiguous to therectangular opening 158. As shown in FIGS. 9A and 9B, the end wall 166has an upper area 172 and a lower tapered area 124 extending inwardly ofupper area 172 of end wall 166 and downwardly relative to upper area 172of end wall 166 and the rectangular opening 158 such that the length offloor 168 is less than the length of rectangular opening 158.

With particular reference to FIG. 9A, the optics cup or cuvette 122 alsoincludes a ribbon liner 174 which extends the full length of end wall164, floor 168, upper area 172 of end wall 166 and lower tapered area124 of end wall 166 to cover the inner surfaces of end wall 164, floor168, upper area 172 of end wall 166 and lower tapered area 124 of endwall 166. Ribbon liner 174 may be referred to as a “wet” ribbon linersince it comes into contact with the liquid sample from all sides.Ribbon liner 174 is preferably made of a reflective material, forexample, aluminum. Ribbon liner 174 may be made from a piece of stampedaluminum which may be pre-shaped to conform to the configuration formedby end wall 164, floor 168, lower tapered area 124 of end wall 166 andupper area 172 of end wall 166 prior to the installation of ribbon liner174 in well 156.

Optics cup or cuvette 122 may be made of a material known to minimizethe leaching of the contaminants from the material that might be excitedby the incident light used in an optical analysis of the sample. Asstated above, optics cup or cuvette 122 may be injection molded and madeof a material, for example, ABS plastic or glass. It is anticipated thatthe UV-light provided in an optical analysis of the sample or specimenin container 123 of optics cup or cuvette 122 be directed into thetapered area 124 of well 156 for the optical analysis of the specimenand be reflected off of the ribbon liner 174, including the lowertapered area 124 of end wall 166. As discussed hereinabove, the materialof optics cup or cuvette 122, the reflective material of ribbon liner174 and the lower tapered area 124 of end wall 166 work in a synergisticmanner to enhance the UV-light reflection to more effectively collectthe fluorescence emission of the samples for the identification andquantification of the organism or micro-organism, e.g., bacteria in thesamples and, at the same time, minimize the background fluorescenceand/or minimize the contamination of the sample fluid from the containeror wetted surfaces of the container. The collection of the fluorescenceemission of the sample from the optics cup or cuvette 122 is discussedin greater detail below.

FIG. 9B illustrates that, alternatively, optics cup or cuvette 122 mayinclude a full liner 176, if light collection from the sidewalls 160 and162, as well as from the end wall 164, floor 168, the lower tapered area124 of end wall 166 and the upper area 172 of end wall 166 is needed forthe optical analysis of a sample. This full liner 176 is shaped andformed to substantially clad or cover the inner surfaces of sidewalls160 and 162, end wall 164, floor 168, lower tapered area 124 of end wall166 and the upper area 172 of end wall 166. The full liner 176 of FIG.9B functions similarly to the ribbon liner 174 in well 156 of optics cupor cuvette 122 of FIG. 9A with regard to the UV-light of the opticalanalyzer.

The ribbon liner 174 of FIG. 9A and full liner 176 of FIG. 9B may bepolished to obtain a desired degree of surface roughness for thereflection of the UV-light in optics cup or cuvette 122. The polishingprocess may either be performed on the reflective material used to formwet ribbon liner 174 or full wet liner 176 either when the reflectivematerial, i.e., aluminum, is in raw sheet form prior to the stamping andforming process or when liners 174 and 176 are formed and inserted intooptics cup or cuvette 122 via a bulk polishing process. That is, thereflective material may either be polished before the stamping andforming process or the stamped parts may be polished.

FIG. 9C illustrates that the wet ribbon liner 174 of FIG. 9A may besecured to optics cup or cuvette 122 via a crimping process. In thisinstance, the one end 178 of wet ribbon liner 174 is bent to conformaround and under the outer contour of the portion of flange 154 formedby end wall 166 and end 178 is fastened to flange 154 via a crimpingprocess which is well-known to those skilled in the art. Even though notshown in FIG. 9C, it is to be appreciated that the opposite end ofribbon liner 174 may be bent to conform around and then under the outercontour of the portion of flange 154 formed by end wall 164 and thenfastened to flange 154 via a crimping process.

It is to be further appreciated that even though not shown, in theinstance when a full liner 176 of FIG. 9B is installed in optics cup orcuvette 122, that this liner 176 may be secured to flange 154 via acrimping process. The full liner 176 may be stamped and folded in aprogressive die and then singulated for installation in optics cup orcuvette 122. Both liners 174 and 176 may be wound on a reel and theoptics cup or cuvette 122 can be easily assembled in an automatedmanufacturing process. That is, the liners 174 and 176 may be on a reelso that a machine can be fed with the reels and the liners inserted intothe optics cup or cuvette 122.

FIGS. 9A and 9B illustrate a reflective material for optics cup orcuvette 122 as being a separate piece that is manufactured, formed andshaped for insertion or installation into well 156 of container 123. Thepresent invention envisions that instead of liners 174 and 176, opticscup or cuvette 122 may be coated with a thin layer of reflectivematerial, as indicated at reference number 180 in FIG. 10. In thisembodiment, optics cup or cuvette 122 may be injection molded with thedesired surface roughness and then coated with a thin layer ofreflective material 180, for example, pure aluminum, by either a vacuummetallization process or by an electroplating process. The industry hasshown that it may be difficult to coat inner surfaces of a containerthat has a certain depth. In this instance, customized electrodes mayneed to be provided to achieve the desired coverage and uniformity ofcoating in the well 156 of container 123 of optics cup or cuvette 122.The coating of reflective material 180 may extend totally along theinner surfaces of sidewalls 160 and 162, end walls 164 and 166 and floor168 of container 123 similar to the full liner 176 of FIG. 9B, or thecoating may extend partially along the inner surfaces of end wall 164,the floor 168, lower tapered area 124 of end wall 166 and the upper area172 of end wall 164 of container 123, similar to the ribbon liner 174 ofFIG. 9A.

FIGS. 11A, 11B, and 11C illustrate additional systems for securingribbon liner 174 in container 123 of optics cup or cuvette 122.Specifically, FIG. 11A illustrates that the ribbon liner 174 may besecured to the portion of flange 170 formed by end wall 164 via aone-way retention tab 175 which is inserted through the ribbon liner 174and flange 170 in a manner known to those skilled in the art. Forexample, for this one-way retention tab, the container 123 has a postwhich has small “teeth” and the liner has a hole or opening and once theliner is positioned over the post, the “teeth” of the post prevent theliner from being moved and, therefore, slipping out of container 123.Even though not shown, it is to be appreciated that the opposite end ofribbon liner 174 may also be attached to the portion of flange 170formed by end wall 166 in a similar manner.

FIG. 11B specifically shows that the one end of ribbon liner 174 may besecured to the portion of flange 170 formed by end wall 164 and that theopposite end of ribbon liner 174 may be secured to the portion of flange170 formed by end wall 166 via heat staked pins 182 and 184. Heat stakedpins 182, 184 are also known to those skilled in the art. For example,in general, a heat stake pin 182, 184 is generally smooth and once theribbon liner 174 is positioned on the pin 182, 184, heat is used todeform the end so that the ribbon liner 174 is prevented from slippingout of the container 123.

FIG. 11C specifically shows that the one end of ribbon liner 174 may besecured in end wall 164 near flange 170 via a snap mechanism 186. Thissnap mechanism 186 may be formed in end wall 164 by stripping the moldedmaterial with a tool. If ribbon liner 174 is made of aluminum, ribbonliner 174 can be held securely in snap mechanism 186 since aluminum isflexible enough that it can be easily snapped into snap mechanism 186.Even though not shown in FIG. 11C, it is to be appreciated that end wall166 also includes a similar snap mechanism 186 for securing the oppositeend of ribbon liner 174 in container 123 of optics cup or cuvette 122.

FIG. 12 illustrates an optics cup or cuvette 188 having a two-piececonstruction including an upper piece 190 and a lower piece 192. Asshown, the upper piece 190 has a rectangular body 193 having arectangular opening 194 contiguous to flange 196, which, in turn, isformed by spaced apart sidewalls 198 and 199 and end walls 200 and 201.Even though not shown, upper piece 190 is also fully opened at thebottom and has an indented portion 202. The lower piece 192 has arectangular opening 204 formed by spaced apart sidewalls 206 and 207 andend walls 208 and 209, and a floor 210. End wall 209 of lower piece 192has a tapered area 212 for re-directing the light. Tapered area 212extends down from the rectangular opening 194 and extends downwardly tofloor 210, thereby making the length of floor 210 less than the lengthof rectangular opening 204.

Both upper piece 190 and lower piece 192 are joined together viaindented portion 202 fitting into the rectangular opening 204 of lowerpiece 192 and these two pieces 190 and 192 may be bonded together via amethod selected from the group consisting of an ultrasonic, butt weldingprocess; an ultrasonic, shear welding process; a press fit process; asnap fit process; and a solvent welding process using either a press orsnap fit for fixing the two pieces 190 and 192 together during thebonding process. In this instance, the lower piece 192 is sufficientlyshallow as to enable the desired critical optical inner surfaces ofspaced apart sidewalls 206 and 207, end walls 208 and 209 and floor 210of lower piece 192 to be coated with a reflective material 180, such asaluminum, preferably via a vacuum metallization process in acost-effective manner compared to some of the disadvantages in using anoptics cup or cuvette 122 with a deep well 156 as discussed hereinabovewith reference to FIG. 10. The upper piece 190 may be regarded as askirt or a slosh shield, thereby preventing the sample from flowing outof the optics cup or cuvette 188.

As may be appreciated, the upper flanges of optics cup or cuvette 122and 188 of the present invention may be used for supporting the opticscup or cuvette 122, 188 on a top surface 150 of a disposable cartridge112 used in magazines 126 for processing the samples and then opticallyanalyzing the samples. Also, the reflective surfaces of the optics cupor cuvette 122 and 188 are such that the UV light from the opticalanalyzer can be directed down into the optics cups or cuvettes andreflected off of the reflective surfaces and tapered areas as discussedin detail below to more efficiently and effectively produce thefluorescence emission necessary in obtaining the required informationfor optically analyzing the specimens for the identification andquantification of, for example, organisms or micro-organisms, e.g.bacteria in the specimens or urine specimens.

The optical analyzer 16 of FIGS. 4A, 4B, and 4C, as disclosed in PCTPatent Application No. PCT/US2008/079533 will now be described. Whilethe drawings show cartridges 12 according to the embodiment illustratedin FIGS. 1A, 1B, and 2, it is recognized that the alternative cartridgeof FIGS. 8A and 8F, along with the optics cup or cuvette design 122and/or 188 of FIGS. 9A-9C, 10, 11A-11C and 12, can also be utilized withthe optical analyzer 16. With reference to FIG. 4A, the optical analyzer16 includes an optics system 44 (shown in greater detail in FIGS. 4B and4C), a thermal control unit (not shown), a drawer 51 which has arotatable table 52 which receives, supports, and rotates a magazine 54containing a plurality of holders 56 for receiving the disposablecartridges 12 in which optics cups or cuvettes 22 contain the processedurine samples which are to be analyzed, and a bar code reader 58 (FIG.4A).

As can be appreciated, a cartridge 12 or 112 that has the optics cups orcuvettes 22, 122 or 188 containing the processed urine sample foroptical analysis are placed into the holders 56 of the magazine 54. FIG.4A illustrates the magazine 54 mounted on the rotatable table 52 beingloaded into the optical analyzer 16. Drawer 51 is pulled out manuallyfor the loading and unloading of magazine 54. Drawer 51 contains thethermal control unit (not shown) and a drive mechanism (not shown).Alignment features on the magazine 54 and drawer 51 allow the operatorto orient the magazine 54 properly on the drive mechanism and thethermal control unit when the magazine 54 is loaded onto the rotatabletable 52. Once the drawer 51 and magazine 54 are manually inserted intothe optical analyzer 16, the drive mechanism rotates the magazine 54 atwhich time a bar code reader station 58 (FIG. 4A) inventories thesamples. A level sensor (not shown) verifies that each optics cup orcuvette 22 contains the correct sample volume. An operator can accessthe optical analyzer 16 when a user interface indicates that all thesamples in the optics cups or cuvettes 22 have been analyzed and drawer51 is prevented from being opened when any of the components of opticalanalyzer 16 are moving or when the UV-light sources of the optics system44 are on.

FIG. 4A illustrates the magazine 54 on rotatable table 52 while beingpositioned within optical analyzer 16. The optical analyzer 16 furtherincludes a mechanical locking system (not shown) which positions thedrawer 51 accurately with respect to the optics system 44. The drivemechanism is configured to automatically rotate the magazine 54 toposition each cartridge 12 into the bar code reader station 58 and intoprecise alignment with the optics system 44. A second mechanical lockingsystem (not shown) is used to secure each optics cup or cuvette 22 inits proper positioning relative to the optics system 44 for opticalanalysis.

FIG. 4A illustrates the thermal control for the optical cups or cuvettes22. Preferably, the temperature of each optics cup or cuvette 22 isdecreased to a temperature which will slow the metabolism of thebacteria while increasing the fluorescence signal. The thermal controlunit 47 which is a thermal electric cooler (TEC) cools a large thermalmass 60 which is located on the rotatable table 52 underneath themagazine 54. The thermal mass 60 (FIG. 4A) is in direct contact with theoptical cups or cuvettes 22.

In an alternative embodiment, the invention includes a system forcooling and controlling the temperature of a sample in the optics cup orcuvettes 22 carried by the disposable cartridges; cuvettes or optics cupof the invention. The system of the invention may find particularapplication in an optical analysis of the specimens in that thefluorescence signal will change with a change of temperature, thusresulting in an inadequate analysis of the specimens.

FIG. 13A illustrates a schematic view, according to one design of theinvention, for a system for delivering water, which cools air, which, inturn, is delivered to cool specimens. More specifically, an opticalanalyzer 16 includes a housing 72 for enclosing a carousel 15 whichsupports a plurality of disposable cartridges (not shown), which, inturn, supports an optics cup or cuvette (not shown) containing aspecimen. A tubing system 74 surrounds the outer periphery of aturntable 80 and includes an upper finned tubing 76 and a lower finnedtubing 78, which carries water around the turntable 80. As indicated byarrow A1 located to the left of FIG. 13A, chilled water from a thermalelectrical cooler (TEC) (not shown) is delivered to upper finned tubing76, and as indicated by arrow A2, located to the right of FIG. 13A, coolwater is delivered from upper finned tubing 76 to the TE cooler orchiller at a rate of about 0.5 to 1.0 gallon per minute. The temperatureof the chilled water delivered to the upper finned tubing 76 ismaintained between ±0.1° C. of a desired temperature for cooling thespecimens. This is achieved by detecting the temperature of the coolwater being delivered to the TE chiller, indicated by arrow A2, andusing this information to adjust the water temperature of the chilledwater being delivered from the TE chiller, indicated by arrow A1, to thetemperature needed to adequately cool down and maintain the samples at adesired temperature. The several thick, black arrows A3 indicate thatthe air surrounding the lower finned tubing 78 is drawn upwardly into aFlatpak fan 82 (i.e., a low profile fan) and the several thick, blackarrows A4 indicate that the air from Flatpak fan 82 travels into theturntable 80 and upwardly into openings 84 of turntable 80 and throughopenings of carousel 15 as indicated by arrows A5.

As best shown in FIG. 14A, an upper surface 86 of carousel 15 has aplurality of sections, some of which are indicated by reference number88. Each section 88 forms a cell and has an opening 90. The cool airdistributed by Flatpak fan 82 traveling from openings 84 of turntable 80travels through openings 90 and into its respective cell of sections 88.As best shown in FIG. 14B, a lower surface 92 of carousel 15 has aninner hub 94, a number of radial ribs 96 extending from inner hub 94 andan outer ring 98 connected to radial ribs 96 and including the pluralityof openings 90 for delivering the cool air into sections 88 mounted tothe upper surface 86 of carousel 15. The openings 90 may be 0.156 inchholes. Since the carousel 15 has around 48 compartments or sections 88,and each compartment or section 88 has an opening 90, then the air flowrate of the jets of cool air being delivered through openings 90 andinto compartments or sections 88 may range from about 15 to 20 cubicfeet per minute.

Referring to FIGS. 14A and 14B, it is to be appreciated that eachsection 88 forming the carousel 15 supports a disposable cartridge 112,similar to the cartridge 112 in FIGS. 2 and 3A. Each disposablecartridge 112 contains a centrifuge tube 118, a pipette tip 120 and adisposable optics cup or cuvette 122 (FIG. 14A) for carrying a specimen.The centrifuge tube 118 and pipette tip 120 are generally used toprepare and process the sample in the disposable optics cup or cuvette122 for an optical analysis of the contaminants, e.g., organisms in thespecimen in the optical analyzer 16 of FIG. 13A. Each cartridge isreceived within a compartment. As can be seen in FIG. 14A, eachcompartment includes a lower recessed lip portion that receives clips113, 115 and 117, as shown in FIG. 8D. Also, the alignment member 116 ofFIG. 8D is adapted to cooperate with one of the adjacent walls definingthe respective compartments that receive the disposable cartridge 112,so that the alignment member contacts one compartment wall and the othercompartment wall contacts the wall 114 opposite the alignment member 116for horizontal alignment. Alignment member 116 is optional and is alsoshown in phantom in FIG. 8E.

Preferably, the turntable 80 is made of aluminum and the disposablecartridges 112 as well as the optics cups or cuvettes 122 are injectionmolded transparent plastic.

FIG. 13B shows a schematic view, according to another design of theinvention, illustrating the pathways for air jets for delivering coolingair to the carousel 15. A pair of TEC modules 278 in the assembly 270cools the “cold plate” 271, 272, 274 as shown in FIG. 15A, which in turncools the surrounding air and this air is supplied to the samples viaair pump or radial fan 279. The cooled air, as shown by arrow A6 issupplied upwardly through at least one or a plurality of openings 284 ofturntable 280 and through openings of carousel 15.

FIG. 15A shows an expanded perspective view of a cold chamber assembly,generally indicated as 270, utilizing the cooling system of FIG. 13B.The cold chamber assembly 270 envelops the carousel 15 and includes a“cold plate”, comprising of a top plate 271, as best shown in FIGS. 15Band 15E, and a bottom plate 272, as best shown in FIG. 15D, separated bya spacer 274. An insulation bottom member 275, as best shown in FIG.15C, is positioned below the bottom plate 272. A pair of apertures 276are provided in the insulation bottom member 275. A TEC module 278extends through each of the apertures 276 to contact the bottom plate272 and to cool it. This air is transferred or fed throughout thecarousel by radial fan 279. A plurality of openings 284 extend throughthe top and bottom plates 271, 272 and the spacer 274 to supply thecooled air to the cell sections 288. A plurality of return openings 285are provided in the top plate 271 to allow for circulation of the coldair through cell sections 288 so that the warmer air is recycled backpast the TEC modules 278 for re-cooling.

As best shown in FIG. 15F, an upper surface 286 of the carousel 15 has aplurality of sections, some of which are indicated by reference number288. Each section 288 forms a cell and the circulation of the cold airis achieved via an inlet opening 290 and an outlet opening 291. Asdiscussed above, the cool air is distributed by a radial fan 279traveling from openings 284 of top and bottom plate 271, 272 and travelsthrough inlet openings 290 and into a respective cell of sections 288and then out through outlet openings 291. The inlet and outlet openings290, 291 may be 0.156 inch holes. Since the carousel 15 has around 40-50compartments or sections 288, and each compartment or section 288 has aninlet opening 290 and an outlet opening 291, then the air flow rate ofthe jets of cool air circulating through inlet and outlet openings 290,291 and into compartments or sections 288 may range from about 15 to 20cubic feet per minute. It can be appreciated that the number ofcompartments or sections 88, 288 can vary.

Referring again to FIGS. 13A, 13B, 14A and 15F, in the optical analyzer16, the carousel 15 made up of the sections 88, 288 is supported by theturntable 80 that locates and positions the optics cups or cuvettes 122(FIGS. 14A, 15F) one by one, under the optical system (not shown). Thecooling system of the invention as described with reference to FIGS. 13Aand 13B is intended to operate to cool the specimen in the optics cup orcuvettes 122 to the desired temperature. For example, each specimen maybe cooled from an ambient temperature down to a desired temperature,e.g., around 25-18° C. within approximately five minutes after start-upof the cooling system of FIGS. 13A and 13B and then the temperature maybe controlled to within ±0.5° C. of the desired temperature until theoptical analysis of the samples is completed. Since the turntable 80 isaluminum, the disposable cartridges 12, 112 and optics cups or cuvettes122 are plastic, and the optics cups or cuvettes 122 are supported inthe disposable cartridges 12, which, in turn, are supported in thesections 88, 288 of the carousel 15, convective cooling is used toassist the cool jet airs traveling through openings 90 and into sections88, 288 in the rapid cooling of the samples.

A further embodiment of the invention envisions a turntable similar tothat described and illustrated above with reference to FIGS. 13A and14A. An aluminum block is located below the turntable and has aplurality of passageways in association with the turntable for carryingchilled air from a TEC module to the turntable and cool air from theturntable and, thus, the carousel, to the TEC module for cooling thesamples and then cooling the temperature of the specimens in a similarmanner described hereinabove with reference to FIGS. 13A and 14A.

The optics system 44 of the optical analyzer 16 will now be described.The optics system is shown in greater detail in FIG. 4B. The opticssystem 44 contains three separate units, that is, an excitation unit44(a), an optical collection unit 44(b) and a spectrometer. Excitationwill be provided by an ultraviolet (UV) light source, which preferablywill be LED (light emitting diode). A series of five LED modules providean excitation unit 44(a) and will sequentially provide excitationsignals to each sample cup or cuvette 22, 122 or 188 at five differentexcitation wavelengths which will be applied to each sample cup orcuvette 22, 122 or 188 in the same order. The excitation time will beapproximately 14 seconds per wavelength. The excitation emissions aredirected via lenses and filters 44(d) to be directed to an upper surfaceof the sample in the cuvette 22, 122 or 188. In order to narrow orcontrol the shape of each excitation wavelength, narrow bandwidthfilters will be used. These filters will direct in a downwardlydirection the excitation wavelengths E to the sample cups or cuvettes 22and the fluorescent emissions F will be reflected back in an upwardlydirection to the optical collection unit from the same position of thecassette. The fluorescent emissions can be separated and directed via afilter arrangement. FIG. 4C illustrates the positioning of the opticssystem 44. As described previously, mechanical locking features positionthe drive mechanism such that the sample cup or cuvette 22 is alignedprecisely. This precise alignment allows for the reflection of thefluorescent emission to the optics system 44 allowing for measurement offluorescence. Optical elements (not shown) are utilized to gather anddirect the fluorescent emissions into the spectrometer for measurement.

In addition, the optical collection unit includes optical elements togather and direct the fluorescent emissions of the samples in the cupsor cuvettes 122 into the spectrometer.

The optics system 44 (FIGS. 4B and 4C) may include a Czerny-Turnerspectrometer with a CCD (charged couple device) Photon Detector, wherebyfluorescent photons are reflected by several mirrors before contactingthe CCD device. The emitted fluorescence will be monitored on the CCDdevice by integrating for a period of time. It is also envisioned thatthe Czerny-Turner spectrometer be modified with additional cylindricallenses adjacent the entrance slit and the CCD device in order to improvephoton usage efficiency. Additionally, as schematically illustrated inFIG. 5, mirrored convex “horn” H may be provided at the entrance of theslit S of the spectrometer SM to direct additional photons through theslit S.

Referring to FIG. 4A, the optics system 44 will include a light-tightenclosure or housing 64 in order to minimize light entering the opticssystem 44, and the camera of the CCD device will include a thermalelectric cooler (TEC) (not shown) for transferring heat from the camerachip to the enclosure or housing 64 of the optics system 44.

The spectrometer of the optics system will now be described. Thearrangement of components for a spectrometer of the invention receivesan illumination beam which exits an optical collection system adjacentan optics cup or cuvette used in an optical analyzer which identifiesand quantifies the presence of contaminants, e.g., bacteria inspecimens.

Referring first to FIG. 16, a spectrometer 300 of the invention is usedin conjunction with an optical collection unit 232 having a plurality oflenses and an optics cup or cuvette 188 containing a urine specimen. Thespectrometer 300 includes a spectrometer slit 302 located immediatelyadjacent to the optical collection unit 232 and a first cylinder lens304 located immediately adjacent to the slit 302 in the same path oftravel for an illumination beam as that of the optical collection unit232 and optics cup or cuvette 188. A first collimating mirror 306 and asecond collimating mirror 308 are located to the far left of the firstcylinder lens 304, and a grating 310 is located to the bottom of opticalcollection unit 232. A second cylinder lens 312 and a CCD sensor 314 arelocated to the left of the grating 310 in FIG. 16.

The illumination beam enters optics cup or cuvette 188 from a lightsource (not shown) in a manner discussed above and fluorescent light isemitted out of optics cup or cuvette 188 and through the lenses of theoptical collection unit 232. From optical collection unit 232, thefluorescence beam travels through the spectrometer slit 302 and throughthe first cylinder lens 304. From first cylinder lens 304, thefluorescence beam travels along a first optical path and toward thefirst light collimating mirror 306. The beam is reflected fromcollimating mirror 306 and travels upon a second optical path throughgrating 310. The fluorescence beam in grating 310 is dispersed into aplurality of dispersed beams which are reflected off of grating 310 andtravel along a third optical path toward the second collimating mirror308. These dispersed beams strike the second collimating mirror 308which, in turn, focuses the dispersed beams toward and through thesecond cylinder lens 312 along a fourth optical path. From the secondcylinder lens 312, the dispersed beams are then received in the CCDsensor 314. The spectral information is captured by the CCD sensor 314for the optical analysis of the urine specimen in optics cup or cuvette188.

The first mirror 306, the second mirror 308 and the grating 310, arepreferably spherical in shape and have a 3-inch diameter. The grating310 preferably is a plane diffraction grating having 1200 lines permillimeter (1 pm) and blazed 10.4° for a 300 nm wavelength region. Suchan appropriate grating is manufactured by and obtained from the NewportCorporation under product Model No. 53-030R.

A grating response for this type of grating 310 is illustrated in FIG.17, wherein line L1 represents the S-Plane, line L2 represents theP-Plane and line L3 represents the average of the S-Plane and theP-Plane. As can be appreciated from the graph of FIG. 21, the bestabsorbent efficiency occurs in the 300 to 400 nm wavelength region,which is the region of interest for the grating necessary in thespectrometer 300 of the invention.

Referring again to FIG. 16, the first cylindrical lens 304 and thesecond cylindrical lens 312 are made of fused silica and are componentsreferred to as components off the shelf or COTS. The first cylindricallens 304 located adjacent spectrometer slit 302 is located approximately10.7 mm from slit 302 and is a CVI Model No. CLCX-15.00-10.2-UV, and thesecond cylindrical lens 312 located adjacent to CCD sensor 314 is a CVIModel No. RCX-400 25.4-15.3-UV.

Still referring to FIG. 16, the first collimating mirror 306 adjacentthe spectrometer slit 302 has a nominal radius of about 400 m and thesecond collimating mirror 308 has a nominal radius of about 350 m. Theratio of the focal lengths of first collimating mirror 306 and secondcollimating mirror 308 is adjusted in order to fit the 300 to 420 nmspectrum of the illumination beam into the chip of the CCD sensor 314.

The CCD sensor 314 may be a Hamamatsu Model No. S7031-1008 chip which isapproximately 25 mm wide and 6 mm long. The CCD sensor 314 preferably isa single-stage cooled unit which uses thermal electrical cooling (TEC).For a bandwidth range of 300-400 nm, which is the wavelength range ofinterest for the present invention, the quantum efficiency of the chipfor the preferred CCD sensor 314 is approximately 50%.

Still referring to FIG. 16, the dimensions for the slit of thespectrometer slit 302 is nominally 2.8 mm wide and 5 mm long. Using asource bandwidth of 10 nm FWHM and a triangular function for the sourceoutput with wavelength, the spectral width of the system of FIG. 16 atthe plane of the CCD sensor 314 is 12.5 nm FWHM. The acceptance angle ofthe spectrometer 300 of FIG. 16 is approximately 0.4 NA(nano-Angstroms).

In the arrangement 300 of the invention, the first cylindrical lens 304tends to capture the additional radiation of the fluorescence beamexiting the spectrometer slit 302 and then direct the radiation throughthe optics system of FIG. 16. The second cylindrical lens 312 in closeproximity to the plane of the CCD sensor 314 tends to focus thisradiation onto the pixels in the CCD plane which are about 6 mm inlength. It is the inventor's position that the combination of the firstcylindrical lens 304 and the second cylindrical lens 312 enhances thethroughput of the spectrometer 300 of FIG. 20 compared to conventionalspectrometers which do not include lenses similar to lenses 304 and 312of the invention.

The spectrometer 300 of FIG. 16 may generally be similar to aCrossed-Czerny-Turner layout with the addition particularly of the firstcylindrical lens 304 and the second cylindrical lens 312 to create a lowresolution (less than 10 nm), but highly sensitive spectrometer for usewith wavelengths in the 300 nm to 420 nm range. The plane of the CCDsensor 314 represents a 25 mm length detector.

The sample processor 14 will have a HEPA air-filtering system forventilation purposes in filtering the air exiting the sample processor14.

It is further envisioned that the LED intensity will be monitored tocorrelate the emitted fluorescence with the intensity of the excitationfluorescence. In particular, the information obtained by the opticalanalyzer 16 may be used to generate graphs similar to FIGS. 5 through 9of U.S. Patent Application Publication No. 2007/0037135 A1, which iscommonly owned and herein incorporated by reference in its entirety,described in greater detail below. The graphs represent for theconcentration of the bacteria in the sample cups or cuvettes 22, thefluorescence intensity, the emission wavelengths and the excitationwavelengths.

An illumination arrangement for exciting and optically collecting lightin the optics cup or cuvette 122 used in an optical analyzer 16 whichidentifies and quantifies the contaminants in the sample is shown inFIGS. 18-21 and is discussed in more detail below.

A known measuring system is shown in U.S. Pat. No. 7,277,175 B2 whichdiscloses a system and method for wavelength selective measurement ofproperties of liquid samples. More specifically, the system includes alight source, an optical delivery system, at least two optical systems,a sample holding assembly, a filter assembly, a transmission system anda detector. The filter assembly may be a group of filters contained in afilter wheel. This system may provide for measuring properties of smallvolume liquid samples that allows the insertion of selective wavelengthfilters in an optical train in the vicinity of the measurement locationin order to increase the signal-to-noise ratio. However, this systemdoes not provide for a compact optical reader having an increasedsignal-to-noise ratio for optically analyzing the bacteria in a urinespecimen.

The present invention provides an improved optics system including anoptical reader that has a compact carriage train arrangement whichproduces and directs collimated light into a specimen for an opticalanalysis, while providing an increased signal-to-noise ratio for animproved analysis of the specimen. Referring first to FIG. 18, anoptical reader 214 of the invention includes an illumination arrangement216, a light source 218 for producing an illumination beam, a firstoptical system 220, a second optical system 221, an anchor shoe 222 anda filter wheel 223 located between the second optical system 221 and theanchor shoe 222. The light source 218 may be Xenon, LED's, deuterium andothers. Even though a filter wheel 223 is shown in FIG. 18, a linearvarying filter may be used. The first optical system 220 includes acarriage 224 having a housing 226 for supporting a turning mirror and afilter (not shown). The second optical system 221 includes a carriage228 having a housing 230 for supporting a turning mirror and a filter(not shown). As shown in FIG. 18, the carriage 224 of the first opticalsystem 220 extends into the housing 230 of the second optical system 221to connect the first optical system 220 to the second optical system221. The carriage 228 of the second optical system 221 extends into thefilter wheel 223 and into the housing 230 of the second optical system221 and into the anchor shoe 222 to connect the second optical system221 to the anchor shoe 222. The anchor shoe 222 includes a turningmirror (not shown) located to the right of a slot 222 a, as shown inFIG. 21, for receiving an optics cup or cuvette 122 containing a fluidsample and an optical collection device 232 located above the slot 222 awhich contains a plurality of lenses (more about which is discussedherein below).

As is generally known to those skilled in the art, a filter is used totransmit light only in particular regions of the spectral and is used tochange or modify the total or relative energy distribution of a beam oflight. A turning mirror is at various location points to change thedirection that the light is traveling. A lens is used for focusing ornon-focusing light thereby allowing different optical effects. A slit isgenerally an opening having a specific shape. The light that passesthrough the slit travels to a grating and into a device, such as a CCDcamera, for detection.

The illumination arrangement 216 of FIG. 18 further includes a filterwheel 223. As disclosed in column 4, lines 10-23 of the above-mentionedU.S. Pat. No. 7,277,175 B2, a filter wheel contains a group of filters,wherein a pre-selected filter may be placed in an optical path ofcollimated electromagnetic radiation. The pre-selected filtersubstantially selects transmission in a predetermined wavelength region.The filters generally are pre-selected based on the desired sample to bemeasured and the width of the spectrum of the absorption (or emission)band arising from the interaction of electromagnetic radiation and thesample. For a biological sample, electromagnetic radiation absorption iscentered at wavelengths (λ) ranging from 200 nm to 800 nm, mostly at 230nm, 260 nm and 280 nm.

The lenses used in the optical collection device 232 may be commercialoff-the-shelf (COTS) components.

FIG. 19 illustrates a typical illumination beam indicated at referencenumeral 234 showing a theoretical simulation of the beam path from alight source to a specimen produced by present day lens arrangements. InFIG. 23, a lamp or light source (not shown) is located to the left of afirst lens system H, I, J and K, and a second lens system isapproximately 8 inches away from the first lens system with the outputat an illumination shoe aperture (not shown) in the system which islocated to the far right in FIG. 19. In the invention, the length ofthis illumination beam 234 of FIG. 19 is reduced by the illuminationarrangement 216 of FIG. 18 wherein the illumination arrangement 216incorporates the filter wheel 223. Filter wheel 223 may carry aplurality of narrow band filters, i.e., in the ultraviolet range. Inthis instance, the radiation from light source 218 of FIG. 18 may berestricted to wavelengths ranging from 260 nm to 300 nm. Alternatively,filter wheel 223 may carry filters that provide the whole light spectrumand associated wavelengths. Also, as discussed herein above, a linearvarying filter may also be used instead of the filter wheel 223. Theturning mirrors (not shown) in the first optical system 220 and thesecond optical system 221 of the illumination arrangement 216 of FIG. 18are custom filters which predominantly reflect the ultraviolet band.

FIG. 18 illustrates a graph of custom filters which are Newport thinfilms provided by Newport Corporation, which are used as turning mirrorsin the first optical system 220 and the second optical system 221 of theillumination arrangement 216 of FIG. 18. As illustrated, these customfilters produce a relatively high reflectance that is about 100, in theultraviolet range that is in wavelengths ranging between 200 nm and 380nm and a low reflectance, i.e., 68 to lower than 10 in the visible light(VIS) and irradiation (IR) ranges, i.e., from about 400 nm to 608 nm.Thus, the filters may be VIS, NIR, and/or FIR rejecting filters.

The optical cup or cuvette 22, PCT Patent Application No.US/2008/079533, also discussed in detail above and used in cartridge 12of FIGS. 1A, 1B and 2, has an elongated cylindrical body and a lowertapered end. In this design, the ultraviolet (UV) light source in theoptical analyzer is directed down the middle of the cuvette and intothis lower tapered end for the optical analysis of the biologicalspecimen. The optical cup or cuvette 122 shown in FIGS. 12A-12C, 13,14A-14C and cup or cuvette 188 shown in FIG. 15, is designed to optimizethe fluorescence sensing of the transmitted light rays in the cup orcuvette 122, 188.

FIG. 21 is a schematic of a side view of the anchor or injection shoe222 and optical collection device 232 of the illumination arrangement216 of FIG. 18, wherein an optics cup or cuvette 122, as discussedabove, is positioned within the slot 222 a of anchor shoe 222.

Referring back to FIGS. 9A, 9B, 10, and 21, an example of the optics cupor cuvette 122 is shown, which may be used in the optical reader of theinvention. The optics cup or cuvette 122 includes a rectangular-shapedcontainer 123 having a lower tapered area 124 and an inner reflectivesurface. The container 123 further includes two parallel spaced-apartsidewalls 160, 162, two spaced-apart end walls 164, 166, and ahorizontal floor 168, and wherein the first end wall 164 includes thetapered area 124 which is contiguous to the horizontal floor 168. Thewidth of the horizontal floor 168 of the optics cup or cuvette 122 isabout 7 mm, the depth of the sidewalls 160, 162 and the second end wall166 is about 18 mm, the depth of the first end wall 164 is about 11 mm,the length of the horizontal floor 168 is about 16 mm and the length ofthe tapered area 124 is about 7 mm. The tapered area 124 is angled atabout a 45° angle relative to the first end wall 164.

Still referring to FIG. 21, the inner surface of optics cup or cuvette122 is reflective and preferably made of aluminum with a high qualitysurface finish, or having a micro-roughness less than 50 angstroms. Theoptics cup or cuvette 122 may be made of a low leaching and fluorescencesignal material, for example, plastic or glass. The optics cup orcuvette 122 may be an injection molded plastic, which may subsequentlybe subjected to a metallization step using evaporated aluminum. Thisapproach will allow a low cost mechanical fabrication with a batchprocess coating. A further approach for manufacturing optics cup orcuvette 122 for use in the invention is to use an aluminum foil linerribbon 174, as shown in FIG. 9A, along the inner surface length of thecontainer 123 which forms to the shape of the first end wall 164, thelower tapered area 124, the floor 168 and the second end wall 166 asdiscussed above. The volume of the liquid specimen contained in theoptics cup or cuvette 122 may be approximately 955 μl.

Referring again to FIG. 21, a line L1 represents the incomingillumination beam. This illumination beam is produced by theillumination arrangement 216 of FIG. 22 and passes through a slit (notshown) which nearly collimates the illumination beam. The slit isapproximately a 4×4 mm square in cross-section and is located in theanchor shoe 222. The illumination beam is reflected into the optics cupor cuvette 122 using a turning mirror 235 located in the anchor shoe 222as discussed herein above. The first surface that a beam L2 encountersis the 45° inner surface of lower tapered area 124 of optics cup orcuvette 122. A reflected beam L3 traverses the optics cup or cuvette 122in the volume of liquid represented by a line L4. Upon striking thereflective inner surface of the second end wall 166, the beam returns tothe reflective inner surface of the 45° lower tapered area 124,fluorescence is emitted upwardly and out of optics cup or cuvette 122and toward the anchor shoe 222. The expansion of the beam is controlledby the optics system of the optical reader 214 (FIG. 18) of theinvention and generally may be about 5×5 mm in cross-section upon itsreturn to the anchor shoe 222.

It is to be appreciated that, in view of the optics cup or cuvette 122,the beam in optics cup or cuvette 122 is directed such that it does notilluminate the bottom or floor 168 of the optics cup or cuvette 122during its traversal in the liquid volume of the specimen. Opticalcollection device 232 located above the slot 222 a contains a pluralityof lenses indicated at 236, 238, 240, and 242 and views the floor 168 ofthe optics cup or cuvette 122 and the liquid in the optics cup orcuvette 122, as indicated by lines L5, L6 and L7 which is representativeof the emitted fluorescent rays in FIG. 21. Approximately 47% of theliquid volume of the specimen is read by the optical fluorescentcollection device 232. By eliminating the illumination of the floor 168of optics cup or cuvette 122 and by restricting the optical collectiondevice 232 to view only the floor 168 and not the sidewalls 160, 162 andend walls 164, 166 of optics cup or cuvette 122 (FIGS. 9A and 9B), thebackground fluorescence of the optics cup or cuvette 122, as seen by theoptical collection device 232, can be minimized or nearly eliminated.Raytrace modeling indicates that a factor of 1000× less noise could betheoretically attainable. This is a huge advantage to achieving highersignal-to-noise ratios. By eliminating the noise of fluorescence fromthe optics cup or cuvette 122, the signal is more prominent, and higherfidelity and sensitivity can be achieved. Transmission of theillumination beam and measurement of the emitted fluorescence may occurin concert per sample or the illumination into the sample may stopduring the measurement of the fluorescence.

The following equation details the SNR (signal-to-noise ratio)calculation:

${SNR} = {\frac{S}{\sqrt{S + B_{f}}} + B_{r}}$

S represents the signal. B_(f) represents background fluorescence andB_(r) represents Raman background which occurs in view of the liquidwater in the specimen. For optical readers of the prior art, thesignal-to-noise ratio (SNR) is approximately 8.1 with over 1.5e6 noisephotons from fluorescence and 1e4 photons from the signal. In the designof the present invention, the noise is expected to be reduced to 1.5e4noise photons, while the signal is expected to increase to about 1.2e4photons. In view of these results, it is anticipated that the SNRproduced by the present invention will be about 73.

As discussed hereinabove, the optical analyzer 16 provides results thatare then used to identify the type of bacteria in the urine samples.This can be done by coupling the optical analyzer 16 to a computermodule (not shown) and feeding in the acquired information of theoptical analyzer 16, such as the fluorescence emission, into thecomputer module. The computer module may perform multivariate analysison the fluorescence excitation-emission matrices of the urine samples toidentify and quantify the urine samples in a manner similar to thatdisclosed in the above U.S. Patent Application Publication No.US/2007/0037135 A1. Here, the system includes a fluorescence excitationmodule which includes an excitation light source, a sample interfacemodule for positioning the sample to receive the light source, afluorescence emission module and a detection device. The computer moduledescribed above is coupled to the fluorescence module. The multivariateanalysis may comprise extended partial least squared analysis foridentification and quantification of the urine samples.

It is still further envisioned that a “homogenitor tube” will be used tomix the different LED packages output into a uniform UV light source. Atypical “homogenitor tube” for use in the invention will be similar tothat known to those skilled in the art.

Reference is now made to FIGS. 22A and 22B which show a cover, generallyindicated as 300, for use with the magazine 26 and carousel 15. Thecover securely fits onto the magazine 26 to allow for transfer of afilled magazine from one location to another. The cover 400 preventssplashing/spilling of the contents from the sample cuvettes 22, 122 andfrom contamination of the specimens. The cover 400 can be formed fromany well known material, such as, for example, Plexiglas, otherpolymeric materials, glass or metal and the like. A handle 402 can besecured to the cover 400 by any known attachment member, such as screws404 and the like. The handle 402 can be removably or permanently securedto the cover 400. The cover 400 cooperates with the magazine 26 and/orcarousel 15 to lock the cover in place. This locking system can be anysystem known in the art. According to one design, a locking key 406extends through the cover 400 and through a central portion 408 of thecarousel 15 and cooperates with a keyway 410 located within this centralportion 408. The central portion 408 of the carousel 15 extends througha central portion of the magazine 26 to lock the magazine between thecover 400 and the base 15′ of the carousel 15. A lifting force can bemanually applied to the locking key 406 to withdraw or retract thelocking key 406 from the keyway 410 and remove the cover 400.

Reference is now made to FIGS. 23A-23D which illustrate an alignmentnotch 416 which cooperates with a sensor system (not shown) to opticallyalign the samples within a magazine 426 with respect to a qualitycontrol cartridge 412, as shown in FIG. 23B. The alignment notch 416extends inwardly from an outer periphery 418 of the base plate 420 of acarousel base assembly, generally illustrated as 415. The alignmentnotch 416 and quality control cartridge 412 provide a fixed location atwhich to initialize testing which, in turn, functions as a startinglocation or an initialization point for the cartridges 12, 112 containedwithin the magazine 426. Testing of the samples within cartridges 12,112 can be performed on each consecutive sample as the magazine426/carousel base assembly 415 rotates to test a predetermined number ofcartridges 12, 112 located within the magazine 426. The carousel baseassembly 415 includes a plurality of slots 428 for receiving thecartridges 12, 112. The alignment notch 416 is located in a qualitycontrol slot 428A that is configured to be capable of only receiving thequality control cartridge 412. Likewise, the quality control cartridge412 is configured differently than the sample receiving cartridges 12,112, so that only it fits within the quality control slot 428A.

The base plate 420 can also include radial alignment indicia 430. Theseindicia 430 can be lines, such as colored or white lines printed on thebase plate 420, or textured lines that are printed or placed on the baseplate 420 within the slots 428, to provide a visual reference to ensureproper radial positioning of the cartridges 12, 112 within slots 428. Animproperly placed cartridge 12, 112 within the magazine 426 will coverthis indicia 430, whereas a properly positioned cartridge 12, 112 willreveal this indicia 430.

The quality control cartridge 412 can also be used as a referencesample. Should testing of the contents of the quality control cartridge412 result in a false positive showing for bacteria, then such showingwould indicate a problem with the testing equipment.

The testing system also includes a circumferential alignment feature ofthe cartridges 12, 112 to optimize the reflected signal of the samplescontained within the cuvettes 22, 122. A typical magazine 426 containsforty-two cartridges 12, 112 which, based upon 360° circular magazine426, roughly estimates to a 9° offset for each cartridge. In order tooptimize the reflectance within the cuvettes, it has been foundadvantageous to fine tune the location of each cartridge 12, 112/cuvette22, 122 with respect to the light emitted from the optical analyzer byrotating the carousel base assembly 415 back and forth along thisapproximate 9° arc until the light in the sample produces a maximumreflected signal. When this reflected signal is maximized, then thecuvette 22, 122 is circumferentially aligned for optimal testing.

Reference is now made to FIGS. 24A and 24B which show a rack assembly440 for holding a plurality of modules 442 for use within the system.The rack assembly 440 includes a cabinet 441 containing a plurality ofvertical and horizontal rails 444, 446. The overall rack assembly 440can include wheels 448 mounted on casters 450. Leveling feet 452 canalso be provided. The rack assembly 440 includes an anti-tipping featurecomprising a plurality of extendable/retractable legs 454 that extendfrom base rail 455 adjacent to a front face 456 of the rack assembly440. After positioning of the rack assembly 440, the legs 454 areextended outwardly from the base rail 455 and in a perpendiculardirection with respect to the vertical rails 444. Extension of legs 454will prevent the storage rack 440 from tipping over when extracting themodules 442. The legs should also be extended before pulling out any ofthe modules 442 from the rack assembly 440. According to a furthermodification, a locking mechanism can be provided that only permits asingle module 442 from being open at one time. Also, a locking mechanismcan be provided which will prevent any of the modules from opening ifanti-tipping legs 454 are not activated or fully extended.

Reference is now made to FIGS. 25A-25C that show a heater, generallyillustrated as 470, for use with the sample processor unit 14. Theheater 470 is used to maintain the processing fluid at approximately 37°C. This processing fluid flush can be added to the samples as needed sothat the samples are maintained and/or remain at body temperature.Maintaining the samples at body temperature prevents the sample fromcrystallizing, which typically occurs as the samples cool. The heater470 includes a top 472, bottom 474 and a body portion 476 extendingtherebetween. A heater cartridge element 478, temperature control probe480 and thermistor probe 482 are surrounded by tubing 484 and a sleeve486, all of which are contained within the body portion 476. The heaterbody 476 is temperature controlled with the heater cartridge element 478and the feedback for the temperature control is the temperature controlprobe 480. Fluid is pumped in the tubing 484 such that a heat transferis taking place and the fluid temperature is changing towards thetemperature of the heater body 476. The heater 470 is located in thepath between the syringe pump 626 and the metering arm or liquiddispensing arm 620, as shown in FIG. 29A.

The centrifuge 31 can include one or more balance tubes 490, as shown inFIG. 26A. These tubes 490 can include a weighted bottom portion 492 sothat their weight is substantially equal to the weight of a filledsample tube. These balance tubes 490 can be strategically positioned inthe centrifuge 31 to distribute the weight of a partially filledcentrifuge 31 and reduce vibration of the centrifuge 31 during rotation.The optimal placement of the balance tubes 490 can be computercontrolled to identify the best location for positioning the tubeswithin the centrifuge based on the number of samples to be processed.FIG. 26B shows an enlarged top portion 494 of the tube 490. This topportion 494 includes shoulders 495, 496 and gripping area 498 locatedbetween shoulders 495 and 496. These shoulders can act as a guide toassist a mechanical arm to grasp the tubes 490 in gripping area 498 fora computer controlled automatic loading of the centrifuge 31. Shoulders495, can also act as stop members for cooperating with the top surfaceof a bucket within a rotor, which is within the centrifuge 31 to holdthe tubes 490 within the openings of the bucket.

As illustrated in FIGS. 27A-27F, a fan and HEPA filter (high efficiencyparticulate air filter) arrangement, generally illustrated as 500, maybe provided for processing heated air through the processor unit 14 tomaintain the air within the processor unit 14 at 37° C. or bodytemperature. This arrangement 500 can be located within housing 27, asshown in FIG. 3A. The HEPA filter prevents the spread of airbornebacterial organisms. Some HEPA filters have an efficiency rating of99.995%, assuring a very high level of protection against airbornedisease transmission. The fan 502 is contained within a housing 504 anda door assembly 506 which allows for access to the filter (not shown). Aguard 510 is provided for guarding the fan duct 512. A feedback controlloop is provided to adjust the fan speed and to control the internal airtemperature at the desired temperature. If the internal temperaturewithin the processor unit 14 becomes too hot, then the fan speed isincreased. Alternatively, if the air temperature becomes too cool, thenthe fan speed is reduced. Additionally, a pressure sensor can beprovided adjacent to the HEPA filter to measure the air pressure exitingtherethrough. When the pressure drop of exiting air becomes high enough,such would indicate that the filter needs to be replaced.

Reference is now made to FIG. 28A which shows a 6-bar linkage transfersystem generally indicated as 600 for transferring the sample tubes fromthe cartridges 12 contained within the magazine 26 to the centrifuge 31.The transfer system 600 includes a tower assembly 610 and a robotassembly 612. This transfer system 600 can replace the rotatable gripper33, 33A shown in FIG. 3A. The transfer system includes a pair of arms602, as shown in FIG. 28B configured for simultaneously removingcentrifuge tubes 18 from both sides of the magazine 26. The arms includea pair of grippers 604, as shown in FIG. 28C, that can each move twotubes 18 to the centrifuge 31 at one time. Accordingly, four tubes 18can be moved with one transfer. Optical sensors 606 can be provided oneach of the arms 602 for sensing the location of the tubes 18 within themagazine 26 and/or to determine if a sample tube 18 is present within aparticular slot in the carousel 15. Since the circumferential locationof the slots on the carousel 15 can be different than thecircumferential location on the centrifuge 31, the 6-bar linkage 600 canadjust the axial distance between grippers 604 to adjust for thisspacing difference. Reference is made to FIG. 28D which shows the changein circumferential spacing from the carousel 15 (α) having a distance(β) to the centrifuge 31 (α½) having a distance (β′).

FIGS. 29A-29C show liquid dispensing arms 620 that include a first end621 connected to a processing fluid source 622 for retrieving anddispensing the processing fluid, such as a buffered saline solution intothe centrifuge tubes 18 via a second end 623 for washing the sample orfor diluting the sample. The dispensing arms 620 cooperate withdischarge ports 625 and are capable of applying a suctioning force forremoving the processing fluid from within the tubes 18 and dischargingthis suctioned fluid through discharge port 625 to a location externalof the system. After washing of the sample, additional process fluid 621can be supplied into the tube 18 until reaching the desired fluid level.The liquid dispensing arms 620/discharge ports 622 shown herein canreplace the fluid transfer arms 35, 35 a and syringe pump dispenserfluid system 37 shown in FIG. 3A. As shown in FIG. 29B, these dispensingarms 620 and discharge ports 625 can be positioned on each side of thecarousel. As viewed in FIG. 29A, each discharge arm 620 can include apipette tip 624 configured for dispensing processing fluid into eachtube 18. Preferably the processing fluid is maintained at bodytemperature of approximately 37° C. via heater 470, as discussed aboveand shown in FIG. 25. A syringe pump 626 is preferably provided forpumping the fluid into the tube. This pipette tip 624 may also be usedfor removing liquid from the tubes and disposing of this liquid into adischarge port external of the system. The dispensing arms 620 arevertically or radially movable and the discharge ports can pivot withrespect to the carousel and can be retracted from the carousel to allowfor removal of the carousel. As shown in FIG. 29C, the discharge ports622 can rely on gravity to discharge the liquid, as shown by 630, into adischarge tank or can utilize a pump to send the discharge to a drain orexternal container 630. The waste disposables, i.e., disposablecartridge 12 and disposable components 18, 20, 22, 24 remain in themagazine 26 for manual removal when the magazine 26 is unloaded inpreparation for the next operation of the sample processor 14 forprocessing the next batch of samples.

It will be understood by one of skill in the art that the fluid samplemay be, for example, a biological, chemical or toxicant sample, e.g.,urine sample which is optically analyzed, for example, for the type andamount of organism or micro-organism, e.g., bacteria in the sample.

The present invention has been described with reference to the preferredembodiments. Obvious modifications and alterations will occur to othersupon reading and understanding the preceding detailed description. It isintended that the invention be construed as including all suchmodifications and alterations.

The invention claimed is:
 1. A system for conducting the identificationand quantification of micro-organisms in a sample, comprising: aplurality of disposable cartridges for holding at least an opticalsample cup or cuvette; a sample processor including a magazine forreceiving the plurality of disposable cartridges and configured toprepare the sample and to transfer the sample into the respectiveoptical sample cup or cuvette of each of the disposable cartridges; anoptical analyzer for receiving the plurality of the disposablecartridges and for analyzing the type and quantity of micro-organismscontained in the fluid samples, the optical analyzer including anexcitation unit and an optical collection unit positioned above theoptical cup or cuvette, wherein the optical cup or cuvette comprises acontainer into which a light travels from the excitation unit forperforming an optical analysis of the sample and a reflective surfacefor enhancing the optical analysis and wherein the container furtherincludes at least one tapered sidewall such that during opticalanalysis, the light is directed downwardly through an open portion ofthe container and into the sample, wherein the at least one taperedsidewall is configured to assist with the optical analysis of the sampleand the reflective surface of the container reflects fluorescentemissions back in an upwardly direction out of the sample and throughthe open portion of the container to the optical collection unit foroptical analysis, and wherein the magazine includes a carousel baseassembly and the optical analyzer includes a light source for applyingthe light to the sample and the optical collection unit includes areceiver for measuring the light emittance from the sample, and whereinthe carousel base assembly is configured to be rotated in at least afirst direction along an arc to adjust a location of the sample withrespect to the applied light until the light emitted from the sampleproduces a maximum signal so that the light emittance signal received bythe receiver is maximized and brought to its highest level ofperformance defining a fine-tuned position of the sample, wherein boththe light source and the receiver are located above the sample, emittinglight at a first wavelength to the sample at the fine-tuned position,and measuring fluorescence emitted from the sample at a secondwavelength.
 2. The system of claim 1, wherein the magazine comprises a360° circular magazine that is configured to contain up to forty-twocartridges and a quality control cartridge.
 3. The system of claim 1,wherein the carousel base assembly is configured to be rotated in thefirst direction and in a second direction which is opposite the firstdirection to maximize the light emittance signal.
 4. A system forconducting the identification and quantification of micro-organisms in asample, comprising: a plurality of disposable cartridges for holding atleast an optical sample cup or cuvette: a sample processor including amagazine for receiving the plurality of disposable cartridges andconfigured to prepare the sample and to transfer the sample into therespective optical sample cup or cuvette of each of the disposablecartridges; an optical analyzer for receiving the plurality of thedisposable cartridges and for analyzing the type and quantity ofmicro-organisms contained in the fluid samples, the optical analyzerincluding an excitation unit and an optical collection unit positionedabove the optical cup or cuvette; and an arrangement for cooling andcontrolling the temperature of the sample, wherein the magazine includesa carousel having a plurality of inlet openings and outlet openings,each associated with one of the disposable cartridges; a turntablehaving a plurality of inlet openings and outlet openings, eachassociated with one of the inlet openings and outlet openings in thecarousel; and an insulation plate located below the turntable, saidinsulation plate including at least one thermal electrical cooler forcooling the air circulated through the inlet openings and outletopenings from the carousel through the turntable for controlling thetemperature of the samples, wherein the optical cup or cuvette comprisesa container into which a light travels from the excitation unit forperforming an optical analysis of the sample and a reflective surfacefor enhancing the optical analysis and wherein the container furtherincludes at least one tapered sidewall such that during opticalanalysis, the light is directed downwardly through an open portion ofthe container and into the sample, wherein the at least one taperedsidewall is configured to assist with the optical analysis of the sampleand the reflective surface of the container reflects fluorescentemissions back in an upwardly direction out of the sample and throughthe open portion of the container to the optical collection unit foroptical analysis.
 5. The system of claim 4, including an anti-tippingsystem for a rack assembly holding a plurality of storage drawers foruse within the sample processor, said rack assembly comprising aplurality of vertical and horizontal rails configured for holding thestorage drawers and a base rail, said anti-tipping system comprising atleast one extendable/retractable leg configured for extending from thebase rail.
 6. The system of claim 4, including a heating device forheating a processing fluid to be added to the sample as needed whenlocated within the magazine and maintaining the sample at a desiredtemperature.
 7. The system of claim 4, including a fan/filterarrangement for use in the processor unit comprising a fan for passingair into and through the processor unit, said air having a predeterminedtemperature for maintaining said predetermined temperature within saidunit, a filter for filtering the air as it passes therethrough and outof the processor unit, and a feedback control loop for adjusting a speedof the fan to maintain the air at the predetermined temperature withinthe processor unit.
 8. The system of claim 4, wherein the sampleprocessor comprises a heating system for heating the sample to apredetermined temperature; a fan/filter arrangement for maintaining thesample at the predetermined temperature; and a transfer arm arrangementfor transferring a tube from the magazine to a centrifuge.
 9. The systemof claim 4, including a liquid dispensing arm, said liquid dispensingarm including a first end associated with a processing fluid, a secondend associated with a tube, and a pump for pumping said processing fluidinto said tube.
 10. A system for conducting the identification andquantification of micro-organisms in a sample, comprising: a pluralityof disposable cartridges for holding at least an optical sample cup orcuvette; a sample processor including a magazine for receiving theplurality of disposable cartridges and configured to prepare the sampleand to transfer the sample into the respective optical sample cup orcuvette of each of the disposable cartridges; an optical analyzer forreceiving the plurality of the disposable cartridges and for analyzingthe type and quantity of micro-organisms contained in the fluid samples,the optical analyzer including an excitation unit and an opticalcollection unit positioned above the optical cup or cuvette; and analignment system for aligning samples within the magazine, saidalignment system comprising at least one notch extending inwardly withrespect to an outer edge surface of the magazine, a quality controlcartridge located adjacent the at least one notch and a sensor fordetecting the location of the notch and the quality control cartridge,wherein the optical cup or cuvette comprises a container into which alight travels from the excitation unit for performing an opticalanalysis of the sample and a reflective surface for enhancing theoptical analysis and wherein the container further includes at least onetapered sidewall such that during optical analysis, the light isdirected downwardly through an open portion of the container and intothe sample, wherein the at least one tapered sidewall is configured toassist with the optical analysis of the sample and the reflectivesurface of the container reflects fluorescent emissions back in anupwardly direction out of the sample and through the open portion of thecontainer to the optical collection unit for optical analysis.
 11. Asystem for conducting the identification and quantification ofmicro-organisms in a sample, comprising: a plurality of disposablecartridges for holding at least an optical sample cup or cuvette; asample processor including a magazine for receiving the plurality ofdisposable cartridges and configured to prepare the sample and totransfer the sample into the respective optical sample cup or cuvette ofeach of the disposable cartridges; an optical analyzer for receiving theplurality of the disposable cartridges and for analyzing the type andquantity of micro-organisms contained in the fluid samples, the opticalanalyzer including an excitation unit and an optical collection unitpositioned above the optical cup or cuvette; and at least one balancetube located within the centrifuge to balance and distribute the weightof the centrifuge to reduce vibration thereof during rotation, whereinthe optical cup or cuvette comprises a container into which a lighttravels from the excitation unit for performing an optical analysis ofthe sample and a reflective surface for enhancing the optical analysisand wherein the container further includes at least one tapered sidewallsuch that during optical analysis, the light is directed downwardlythrough an open portion of the container and into the sample, whereinthe at least one tapered sidewall is configured to assist with theoptical analysis of the sample and the reflective surface of thecontainer reflects fluorescent emissions back in an upwardly directionout of the sample and through the open portion of the container to theoptical collection unit for optical analysis.